The problem of the underrepresentation of girls in science in Australian schools is often attributed to their poor performance. Yet the role of both the home and the school in affecting female science achievement is rarely examined empirically. The comprehensiveness of the Second International Science Study database provided an excellent opportunity to investigate the presence of gender differences in science achievement. Although previous studies of gender differences in science achievement have relied on methodology that has not adequately accounted for the school effects, this study used the design effect and hierarchical linear modeling (multilevel analysis) to explore whether there were significant gender differences. The relative contribution of schools to student achievement was examined, and school-level differences were found to contribute significantly toward explaining variations in student performance. Although statistically significant sex differences were found in physics achievement for 10-year-old, 14-year-old, and year-12 students, school effects were much more powerful in explaining student differences (9–19%) when compared with gender (3%).